Brock Biology of Microorganisms (15th Edition)
15th Edition
ISBN: 9780134261928
Author: Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, David A. Stahl
Publisher: PEARSON
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Chapter 15.1, Problem 2MQ
- What are three reasons that functional traits might not correspond with distinct phylogenetic groups as defined by 16S ribosomal RNA gene sequences?
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The phylogenetic tree of the OCTN homologs below was generated with the following accession numbers as basis:
NP_957143.1 - OCTN of unknown function
CDM63451.1 - OCTN specific for ergothioneine transport
XP_021324939.1 - OCTN specific for carnitine transport
Design the phylogenetic tree to make it look more interesting by highlighting the distinct clades or putting a visual emphasis on the gene you are trying to analyze. Provide a caption for this figure.
Explain how the different “-omics” involved with the three major parts of the central dogma can be used to study this new species. What are molecular techniques/tools (sequencers) that can be used to study each of these? How would you sequence the genome efficiently (i.e., lowest amount of time and money)?
Here is some information about the sequences:
There are two images given; one with sequences and the other with a figure.
All these sequences, “SEQUENCE_21” to “SEQUENCE_27” are in the same subfamily or “clade” of a large phylogenetic alignment of all Rab proteins in these three species (see “Image with a figure” for a full view of gene family in humans, plants and yeast, see the “D” branch towards the bottom of the tree in Figure). “SEQUENCE_28” is a different Rab protein (actually it is the Rab39 protein at the bottom of the tree).
“SEQUENCE_21” is from yeast.
“SEQUENCE_22” to “SEQUENCE_25” are from the plant, Arabidopsis.
“SEQUENCE_26” and “SEQUENCE_27” are from humans.
Question: Based on the information above, what can you speculate about the possible evolution of the genes that “SEQUENCE_21” to “SEQUENCE_27” represent?
Chapter 15 Solutions
Brock Biology of Microorganisms (15th Edition)
Ch. 15.1 - Why is it necessary to consider microbial...Ch. 15.1 - What are three reasons that functional traits...Ch. 15.1 - What is convergent evolution and how is it...Ch. 15.2 - What form of photosynthesis was most likely the...Ch. 15.2 - Which bacterial phyla contain phototrophs?Ch. 15.3 - What are the differentiating properties of the...Ch. 15.3 - Prob. 2MQCh. 15.3 - How are prochlorophytes, such as Prochlorococcus,...Ch. 15.4 - What is the source of the purple color from which...Ch. 15.4 - Prob. 2MQ
Ch. 15.4 - Compare and contrast the metabolism, morphology,...Ch. 15.5 - What are some similarities between purple...Ch. 15.5 - Prob. 2MQCh. 15.5 - Compare and contrast the metabolism of purple...Ch. 15.6 - Prob. 1MQCh. 15.6 - Prob. 2MQCh. 15.6 - Prob. 1CRCh. 15.7 - Prob. 1MQCh. 15.7 - Prob. 2MQCh. 15.7 - Prob. 1CRCh. 15.8 - What types of anoxygenic phototrophs contain...Ch. 15.8 - Prob. 2MQCh. 15.8 - In what ways is Chloracidobacterium thermophilum...Ch. 15.9 - What are the typical electron donors used by...Ch. 15.9 - What bacterial phyla are known to contain...Ch. 15.9 - Prob. 1CRCh. 15.10 - What are the typical electron donors used by...Ch. 15.10 - Prob. 2MQCh. 15.10 - In what ways are sulfur-reducing bacteria...Ch. 15.11 - Describe the energy and carbon metabolism of...Ch. 15.11 - What are some ecological strategies that sulfur...Ch. 15.11 - Prob. 1CRCh. 15.12 - What mechanisms do free-living diazotraphs use to...Ch. 15.12 - Prob. 2MQCh. 15.12 - What are some ways that diazotrophs protect...Ch. 15.13 - Under what conditions would you expect...Ch. 15.13 - Prob. 2MQCh. 15.13 - Prob. 1CRCh. 15.14 - In what phylogenetic groups are Geobacter and...Ch. 15.14 - Prob. 2MQCh. 15.14 - Prob. 1CRCh. 15.15 - What habitat characteristics govern the diversity...Ch. 15.15 - How do aerobic neutrophilic iron-oxidizers keep...Ch. 15.15 - Prob. 1CRCh. 15.16 - What is the difference between a methanotroph and...Ch. 15.16 - What is unique about the methanotroph...Ch. 15.16 - What are the differences between type I and type...Ch. 15.17 - Prob. 1MQCh. 15.17 - What are the different ways in which species of...Ch. 15.17 - Compare and contrast the life cycle of Myxococcus...Ch. 15.18 - Prob. 1MQCh. 15.18 - Prob. 2MQCh. 15.18 - Prob. 1CRCh. 15.19 - What are the major differences between spirochetes...Ch. 15.19 - Name two diseases of humans caused by spirochetes.Ch. 15.19 - Contrast the motility of spirochetes with that of...Ch. 15.20 - Prob. 1MQCh. 15.20 - Prob. 2MQCh. 15.20 - Contrast the life cycle of Hyphomicrobium with...Ch. 15.21 - Describe how a sheathed bacterium such as...Ch. 15.21 - List two metals that are oxidized by sheathed...Ch. 15.21 - In what environment might you expect to find...Ch. 15.22 - What benefit do magnetic bacteria accrue from...Ch. 15.22 - Would you expect to find greigite or magnetite in...Ch. 15.22 - In what way does a magnetosome contribute to the...Ch. 15 - Describe a key physiological feature of the...Ch. 15 - Describe the metabolism for each of the following...Ch. 15 - Using an example from each of the morphologically...
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- List three reasons why rRNA genes are suitable for phylogeneticanalyses.arrow_forwardHere is some information about the sequences: All these sequences, “SEQUENCE_21” to “SEQUENCE_27” are in the same subfamily or “clade” of a large phylogenetic alignment of all Rab proteins in these three species (see “Figure 1.pdf” for a full view of gene family in humans, plants and yeast, see the “D” branch towards the bottom of the tree in Figure 1). “SEQUENCE_28” is a different Rab protein (actually it is the Rab39 protein at the bottom of the tree). “SEQUENCE_21” is from yeast. “SEQUENCE_22” to “SEQUENCE_25” are from the plant, Arabidopsis. “SEQUENCE_26” and “SEQUENCE_27” are from humans. Question: Based on the information above, what can you speculate about the possible evolution of the genes that “SEQUENCE_21” to “SEQUENCE_27” represent? (write 5 points at least).arrow_forwardHow do the following genomic features of prokaryotic organisms compare with those of eukaryotic organisms? How do they compare among eukaryotes? a. Genome size b. Number of genes c. Gene density (bp/gene) d. Number of exonsarrow_forward
- Why is sequence alignment critical to phylogenetic analysis?arrow_forwardCarl Woese has recognized that genes encoding rRNAs are excellent candidates for phylogenetic analysis. Identify at least 4 characteristics/properties of these rRNA genes which make them good molecular chronometers.arrow_forwardCarl Woese discovered that genes encoded for rRNAs are good candidates for phylogenetic analysis. Determine at least four characteristics/properties of these rRNA genes that make them effective molecular chronometers.arrow_forward
- What are molecular scissors? Explain their role.arrow_forwardWhen comparing evolutionary similarities between different genes within a gene family, it is usually more straightforward to compare genes by using the protein sequences of gene products rather than DNA sequences of the genes themselves. Explain why this is the case. (Include 4 succinct points at least)arrow_forwardWhat is the major difference in how duplicationshave contributed to the evolution of the genomes ofprokaryotic and eukaryotic cells?arrow_forward
- What are some reasons why, in multicellular eukaryotes, genome size is not necessarily related to number of protein-coding genes or organismal complexity?arrow_forwardThe following two sequences represent the same gene from two different species: Assume that all changes in the third position are synonymous and all in the first and second positions are nonsynonymous. a) How many synonymous sites (positions) are there in the gene? b) How many nonsynonymous sites (positions) are there in the gene? c) How many synonymous substitutions are there between species? d) How many nonsynonymous substitutions are there between species? e) What is the dN/dS ratio? f) What does the dN/dS ratio tell you about the evolution of this sequence? Finally, It has been hypothesized that population size affects genome size. What is the proposed relationship? How can it be explained?arrow_forward2b)An ancient gene underwent duplication during the course of evolution to yield two chain genes designated as δ and ε genes. Jessica’s final year project deals with the metagenomic studies of anfH homologous genes from freshwater lake samples in Kampar Eastlake. She successfully cloned and sequenced two partial anfH homologous gene sequences.BlastX analyses revealed that one of the DNA sequences showed highestsimilarity to AnfH protein from a Brazilian soil bacteria isolate while the second sequence showed highest identity to the AnfH protein sequence of a bacterium that was isolated from Tonle Sap, a freshwater lake in Cambodia. To determine their evolutionary relationship, she subsequently constructed a phylogenetic tree using the corresponding protein sequences. Describe the steps that are required toperform the analysis.arrow_forward
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